Genotyping, sequencing and analysis of 140,000 adults from Mexico City

The Mexico City Prospective Study is a prospective cohort of more than 150,000 adults recruited two decades ago from the urban districts of Coyoacán and Iztapalapa in Mexico City1. Here we generated genotype and exome-sequencing data for all individuals and whole-genome sequencing data for 9,950 selected individuals. We describe high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Indigenous American, European and African ancestry, with extensive admixture from Indigenous populations in central, southern and southeastern Mexico. Indigenous Mexican segments of the genome had lower levels of coding variation but an excess of homozygous loss-of-function variants compared with segments of African and European origin. We estimated ancestry-specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Indigenous Mexican ancestry at exome variants, all available through a public browser. Using whole-genome sequencing, we developed an imputation reference panel that outperforms existing panels at common variants in individuals with high proportions of central, southern and southeastern Indigenous Mexican ancestry. Our work illustrates the value of genetic studies in diverse populations and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States, where the Hispanic/Latino population is predominantly of Mexican descent

The influenza A(H1N1) epidemic in Mexico. Lessons learned

Abstract Several influenza pandemics have taken place throughout history and it was assumed that the pandemic would emerge from a new human virus resulting from the adaptation of an avian virus strain. Mexico, since 2003 had developed a National Preparedness and Response Plan for an Influenza Pandemic focused in risk communication, health promotion, healthcare, epidemiological surveillance, strategic stockpile, research and development. This plan was challenged on April 2009, when a new influenza A(H1N1) strain of swine origen was detected in Mexico. The situation faced, the decisions and actions taken, allowed to control the first epidemic wave in the country. This document describes the critical moments faced and explicitly point out the lessons learned focused on the decided support by the government, the National Pandemic Influenza Plan, the coordination among all the government levels, the presence and solidarity of international organizations with timely and daily information, diagnosis and the positive effect on the population following the preventive hygienic measures recommended by the health authorities. The international community will be able to use the Mexican experience in the interest of global health.</p

The burden of influenza A and B in Mexico from the year 2010 to 2013: An observational, retrospective, database study, on records from the Directorate General of Epidemiology database

Despite vaccination programs, influenza still represents a significant disease burden in Mexico. We conducted an observational, retrospective analysis to better understand the epidemiological situation of the influenza virus in Mexico. Analysis of the seasonal patterns of influenza A and B were based on the Directorate General of Epidemiology dataset of influenza-like illness(ILI), and severe acute respiratory infection(SARI) that were recorded between January 2010 and December 2013. Our objectives were 1) to describe influenza A and B activity, by age group, and subtype and, 2) to analyze the number of laboratory-confirmed cases presenting with ILI by influenza type, the regional distribution of influenza, and its clinical features. Three periods of influenza activity were captured: August 2010–January 2011, December 2011–March 2012, and October 2012–March 2013. Cases were reported throughout Mexico, with 50.3% (n = 10,320) of cases found in 18–49 year olds. Over the entire capture period, a total of 76,085 ILI/SARI episodes had swab samples analyzed for influenza, 27% were positive. During the same period, influenza A cases were higher in the 18–49 years old, and influenza B cases in both 5–17 and 18–49 age groups. Peak activity occurred in January 2012 (n = 4,159) and December 2012 (n = 348) for influenza A and B respectively. This analysis confirms that influenza is an important respiratory pathogen for children and adults in Mexico despite vaccination recommendations. School-age children and adolescents were more prone to influenza B infection; while younger adults were susceptible to both influenza A and B viruses. Over the seasons, influenza A and B co-circulated

Elimination of Onchocerciasis from Mexico.

BACKGROUND:Mexico is one of the six countries formerly endemic for onchocerciasis in Latin America. Transmission has been interrupted in the three endemic foci of that country and mass drug distribution has ceased. Three years after mass drug distribution ended, post-treatment surveillance (PTS) surveys were undertaken which employed entomological indicators to check for transmission recrudescence. METHODOLOGY/PRINCIPAL FINDINGS:In-depth entomologic assessments were performed in 18 communities in the three endemic foci of Mexico. None of the 108,212 Simulium ochraceum s.l. collected from the three foci were found to contain parasite DNA when tested by polymerase chain reaction-enzyme-linked immunosorbent assay (PCR-ELISA), resulting in a maximum upper bound of the 95% confidence interval (95%-ULCI) of the infective rate in the vectors of 0.035/2,000 flies examined. This is an order of magnitude below the threshold of a 95%-ULCI of less than one infective fly per 2,000 flies tested, the current entomological criterion for interruption of transmission developed by the international community. The point estimate of seasonal transmission potential (STP) was zero, and the upper bound of the 95% confidence interval for the STP ranged from 1.2 to 1.7 L3/person/season in the different foci. This value is below all previous estimates for the minimum transmission potential required to maintain the parasite population. CONCLUSIONS/SIGNIFICANCE:The results from the in-depth entomological post treatment surveillance surveys strongly suggest that transmission has not resumed in the three foci of Mexico during the three years since the last distribution of ivermectin occurred; it was concluded that transmission remains undetectable without intervention, and Onchocerca volvulus has been eliminated from Mexico

Integrated view of Vibrio cholerae in the Americas

International audienceLatin America has experienced two of the largest cholera epidemics in modern history; one in 1991 and the other in 2010. However, confusion still surrounds the relationships between globally circulating pandemic Vibrio cholerae clones and local bacterial populations. We used whole-genome sequencing to characterize cholera across the Americas over a 40-year time span. We found that both epidemics were the result of intercontinental introductions of seventh pandemic El Tor V. cholerae and that at least seven lineages local to the Americas are associated with disease that differs epidemiologically from epidemic cholera. Our results consolidate historical accounts of pandemic cholera with data to show the importance of local lineages, presenting an integrated view of cholera that is important to the design of future disease control strategies

Economic and Disease Burden of Dengue in Mexico

<div><p>Background</p><p>Dengue imposes a substantial economic and disease burden in most tropical and subtropical countries. Dengue incidence and severity have dramatically increased in Mexico during the past decades. Having objective and comparable estimates of the economic burden of dengue is essential to inform health policy, increase disease awareness, and assess the impact of dengue prevention and control technologies.</p><p>Methods and Findings</p><p>We estimated the annual economic and disease burden of dengue in Mexico for the years 2010–2011. We merged multiple data sources, including a prospective cohort study; patient interviews and macro-costing from major hospitals; surveillance, budget, and health data from the Ministry of Health; WHO cost estimates; and available literature. We conducted a probabilistic sensitivity analysis using Monte Carlo simulations to derive 95% certainty levels (CL) for our estimates. Results suggest that Mexico had about 139,000 (95%CL: 128,000–253,000) symptomatic and 119 (95%CL: 75–171) fatal dengue episodes annually on average (2010–2011), compared to an average of 30,941 symptomatic and 59 fatal dengue episodes reported. The annual cost, including surveillance and vector control, was US$170 (95$1.56 (95%CL: 1.38–2.68) per capita, comparable to other countries in the region. Of this, $87 (95$0.80 per capita (95%CL: 0.62–1.12) corresponds to illness. Annual disease burden averaged 65 (95%CL: 36–99) disability-adjusted life years (DALYs) per million population. Inclusion of long-term sequelae, co-morbidities, impact on tourism, and health system disruption during outbreaks would further increase estimated economic and disease burden.</p><p>Conclusion</p><p>With this study, Mexico joins Panama, Puerto Rico, Nicaragua, and Thailand as the only countries or areas worldwide with comprehensive (illness and preventive) empirical estimates of dengue burden. Burden varies annually; during an outbreak, dengue burden may be significantly higher than that of the pre-vaccine level of rotavirus diarrhea. In sum, Mexico’s potential economic benefits from dengue control would be substantial.</p></div

Entomological parameters in the three foci of onchocerciasis in Mexico.

<p>* Northern Chiapas: El Ambar, Alta Gracia, Chimix, and Nueva Esperanza; Oaxaca: Santiago Teotlaxco, Tiltepec, San Miguel Reagui, Santiago Lalopa, La Chichina, and La Esperanza Comaltepec; Southern Chiapas: Brasil, Mexiquito, Jose Maria Morelos, Estrella Roja, Ampliación Malvinas, Las Golondrinas, Las Nubes II, and Nueva América.</p><p>^§ Each pool contained a maximum of 50 flies.</p><p>^& Each pool contained a maximum of 200 flies.</p><p>^¶ The upper value represents point estimate and the lower value in parentheses represents the 95%-confidence interval.</p><p>Entomological parameters in the three foci of onchocerciasis in Mexico.</p

Mass drug administration (MDA) with ivermectin in two endemic foci: Coverage rate, expressed in percent, of the eligible population.

<p>The eligible population excluded pregnant and lactating women and children under 5 years of age. These groups represented 9.5% of the total population during the last year of MDA in the Southern Chiapas focus in 2011. Panel A: Semi-annual treatment regimen was employed in Northern Chiapas from 2000 through 2007 when MDA ceased. Panels B-C. Semi-annual regimen was employed in Southern Chiapas from 1995 through 2011 (Panel B; Figure taken from Rodriguez-Perez et al., 2013 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003922#pntd.0003922.ref018" target="_blank">18</a>]); in addition, quarterly treatment was employed in 50 communities from 2003 through 2008 and in 163 communities from 2009 through 2011 when MDA ceased (Panel C). The semi-annual treatment regimen was employed in Oaxaca from 1996 through 2008 when MDA ceased (see <a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003922#pntd.0003922.g002" target="_blank">Fig 2</a> in Rodriguez-Perez et al., 2010 [<a href="http://www.plosntds.org/article/info:doi/10.1371/journal.pntd.0003922#pntd.0003922.ref020" target="_blank">20</a>]). The line at 85% indicates the coverage needed to be maintained in order to interrupt transmission.</p